ArticleBioData mining2011
A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR.
Article in BioData mining, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability.PeerJ · 2023Article
- GSTM3 variant is a novel genetic modifier in Brugada syndrome, a disease with risk of sudden cardiac death.EBioMedicine · 2020Article
- Cutting Edge: Chronic NF-κB Activation in CD4+ T Cells in Rheumatoid Arthritis Is Genetically Determined by HLA Risk Alleles.Journal of immunology (Baltimore, Md. : 1950) · 2015Article
- Use of autocorrelation scanning in DNA copy number analysis.Bioinformatics (Oxford, England) · 2013Article
- Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis.PloS one · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variants are >1 kb genomic amplifications or deletions that can be identified using array platforms. However, arrays produce substantial background noise that contributes to high false discovery rates of variants. We hypothesized that quantitative PCR could finitely determine copy number and assess the validity of calling algorithms.
resultsUsing data from 29 Affymetrix SNP 6.0 arrays, we determined copy numbers using three programs: Partek Genomics Suite, Affymetrix Genotyping Console 2.0 and Birdsuite. We compared array calls at 25 chromosomal regions to those determined by qPCR and found nearly identical calls in regions of copy number 2. Conversely, agreement differed in regions called variant by at least one method. The highest overall agreement in calls, 91%, was between Birdsuite and quantitative PCR. Partek Genomics Suite calls agreed with quantitative PCR 76% of the time while the agreement of Affymetrix Genotyping Console 2.0 with quantitative PCR was 79%.
conclusionsIn 38 independent samples, 96% of Birdsuite calls agreed with quantitative PCR. Analysis of three copy number calling programs and quantitative PCR showed Birdsuite to have the greatest agreement with quantitative PCR.
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Registered trials
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